graphing sequence similarity

Steve Thompson: VADMS genetics THOMPSON at WSUVMS1.CSC.WSU.EDU
Tue Mar 2 13:22:05 EST 1993

William_D_WARREN at umail.umd.edu in Message-Id:
<9303020004.AA14577 at umailsrv0.UMD.EDU> writes:

>...What I'm lookng for is a program that will take a pair of aligned
>sequences, and plot graphically, either the similarity or identity,
>and using a specifible window size, along the entire length of an
>alignment. By doing this it would me far easier to see the regions
>of high or low similarity/identity and see their relative location
>along the length of the alignment....

If you have access to GCG, their program PlotSimilarity does exactly this.   
It will also deal with multiple sequence alignments and has many built-in
options as well as being able to take advantage of the extensive graphics
capabilities of the Figure program.

					Happy plotting, Steve T

                              Steven M. Thompson
            Consultant in Molecular Genetics and Sequence Analysis
VADMS (Visualization, Analysis & Design in the Molecular Sciences) Laboratory
           Washington State University, Pullman, WA 99164-1224, USA
          AT&Tnet:  (509) 335-0533 or 335-3179  FAX:  (509) 335-0540
                  BITnet:  THOMPSON at WSUVMS1 or STEVET at WSUVM1
                   INTERnet:  THOMPSON at wsuvms1.csc.wsu.edu

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